\name{homogenizeData}
\alias{homogenizeData}
\title{Take two expression matrices and return homogenized versions of the matrices.}
\usage{
homogenizeData(testExprMat, trainExprMat, batchCorrect = "eb",
  selection = -1, printOutput = TRUE)
}
\arguments{
  \item{testExprData}{Gene expression matrix for samples on
  which we wish to predict a phenotype. Gene names as rows,
  samples names as columns.}

  \item{trainingExprData}{Gene expression matrix for
  samples for which we the phenotype is already known.}

  \item{batchCorrect}{The type of batch correction to be
  used. Options are "eb" for Combat, "none", or "qn" for
  quantile normalization.}

  \item{selection}{parameter can be used to specify how
  duplicates are handled, by default value -1 means ask the
  user. 1 means summarize duplictes by their mean and 2
  means to disguard all duplicate genes.}

  \item{Set}{to FALSE to supress output}
}
\value{
a list containing two entries $train and $test, which are
the homogenized input matrices.
}
\description{
This function accepts two expression matrices, with gene
ids as rownames() and sample ids as colnames(). It will
deal with duplicate gene ids. subset and order the matrices
correctly. and perform homogenize the data using whatever
method is specified (by default Combat from the sva
library).
}
\keyword{data}
\keyword{expression}
\keyword{homogenize}

